Locus 871

Sequence ID	X_DroMel_CAF1
Location	2,449,397 – 2,449,546
Length	149
Max. P	0.975629

overview

Window 2

Location	2,449,397 – 2,449,506
Length	109
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	89.92
Mean single sequence MFE	-40.30
Consensus MFE	-31.59
Energy contribution	-33.59
Covariance contribution	2.00
Combinations/Pair	1.00
Mean z-score	-3.73
Structure conservation index	0.78
SVM decision value	1.19
SVM RNA-class probability	0.928909
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2449397 109 - 22224390
CUCGCUUUGUUUGUUUUCUUUUUUCGCAACUAACUGCGAGAAAAUGAAAAUGCAUGCAACGCUCCAGCGAUUGCAGGGCAGUGCACAAAAUCGAAUACAGUU--UGGCGAG---------
((((((....((((.(((((((((((((......))))))))))((....(((.((((((((....))).)))))..)))...)).......))).))))..--.))))))--------- ( -37.80)
>DroSec_CAF1 9965 117 - 1
---GCUUUGUUUGUUUUCUUUUUUCGCAACUAACUGCGAGAAAAUGAAAAUGAAUGCAACGCUCCAGCGAUUGCAGGGCAGUGCACAAAAUCGAAUACAGUGGGUGGCUAGUGCACACAU
---((((((((..(((((((((((((((......)))))))))).)))))..)))(((((((....))).))))))))).((((((...(((.(......).))).....)))))).... ( -41.00)
>DroSim_CAF1 12354 117 - 1
---GCUUUGUUUGUUUUCUUUUUUCGCAACUAACUGCGAGAAAAUGAAAAUGAAUGCAACGCUCCAGCGAUUGCAGGGCAGUGCACAAAAUCGAAUACAGUGGGUGGCUGGUGCACACAU
---((((((((..(((((((((((((((......)))))))))).)))))..)))(((((((....))).))))))))).((((((...(((.(......).))).....)))))).... ( -42.10)
>consensus
___GCUUUGUUUGUUUUCUUUUUUCGCAACUAACUGCGAGAAAAUGAAAAUGAAUGCAACGCUCCAGCGAUUGCAGGGCAGUGCACAAAAUCGAAUACAGUGGGUGGCUAGUGCACACAU
...(((((((((((((((((((((((((......)))))))))).))))))))))(((((((....))).))))))))).((((((........................)))))).... (-31.59 = -33.59 +   2.00)

alignment

secondary structure

dotplot

Window 3

Location	2,449,426 – 2,449,546
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	96.63
Mean single sequence MFE	-32.30
Consensus MFE	-29.79
Energy contribution	-29.57
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-2.30
Structure conservation index	0.92
SVM decision value	0.95
SVM RNA-class probability	0.888684
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2449426 120 + 22224390
UGCCCUGCAAUCGCUGGAGCGUUGCAUGCAUUUUCAUUUUCUCGCAGUUAGUUGCGAAAAAAGAAAACAAACAAAGCGAGCGAAUGAGAGGCGCAAUAUAUAGUAUAGUAAAGUGCUAUU
(((..(((((.(((....)))))))).((.(((((((((.(((((.(((.(((............))).)))...))))).))))))))))))))....(((((((......))))))). ( -35.60)
>DroSec_CAF1 10005 116 + 1
UGCCCUGCAAUCGCUGGAGCGUUGCAUUCAUUUUCAUUUUCUCGCAGUUAGUUGCGAAAAAAGAAAACAAACAAAGC----GAAUGAGAGGCGCAAUAUAUAGUAUAGUAAAGUGCUAUU
((((((.((.((((((((((...)).))).(((((.((((.((((((....)))))).))))))))).......)))----)).))..))).)))....(((((((......))))))). ( -30.90)
>DroSim_CAF1 12394 116 + 1
UGCCCUGCAAUCGCUGGAGCGUUGCAUUCAUUUUCAUUUUCUCGCAGUUAGUUGCGAAAAAAGAAAACAAACAAAGC----GAAUGAGAGGCGCGAUAUAUAGUAUAGUAAAGUGCUAUU
.(((((.((.((((((((((...)).))).(((((.((((.((((((....)))))).))))))))).......)))----)).)))).))).......(((((((......))))))). ( -30.40)
>consensus
UGCCCUGCAAUCGCUGGAGCGUUGCAUUCAUUUUCAUUUUCUCGCAGUUAGUUGCGAAAAAAGAAAACAAACAAAGC____GAAUGAGAGGCGCAAUAUAUAGUAUAGUAAAGUGCUAUU
((((((((((.(((....))))))).....(((((.((((.((((((....)))))).))))))))).....................))).)))....(((((((......))))))). (-29.79 = -29.57 +  -0.22)

alignment

secondary structure

dotplot

Window 4

Location	2,449,426 – 2,449,546
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	96.63
Mean single sequence MFE	-34.77
Consensus MFE	-32.13
Energy contribution	-32.47
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-4.03
Structure conservation index	0.92
SVM decision value	1.75
SVM RNA-class probability	0.975629
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2449426 120 - 22224390
AAUAGCACUUUACUAUACUAUAUAUUGCGCCUCUCAUUCGCUCGCUUUGUUUGUUUUCUUUUUUCGCAACUAACUGCGAGAAAAUGAAAAUGCAUGCAACGCUCCAGCGAUUGCAGGGCA
....(((...((........))...)))((((..((.(((((.((.((((.(((((((((((((((((......)))))))))).))))..))).)))).))...))))).))..)))). ( -37.00)
>DroSec_CAF1 10005 116 - 1
AAUAGCACUUUACUAUACUAUAUAUUGCGCCUCUCAUUC----GCUUUGUUUGUUUUCUUUUUUCGCAACUAACUGCGAGAAAAUGAAAAUGAAUGCAACGCUCCAGCGAUUGCAGGGCA
....(((...((........))...)))((((..((.((----(((..(((..(((((((((((((((......)))))))))).)))))..)))((...))...))))).))..)))). ( -33.80)
>DroSim_CAF1 12394 116 - 1
AAUAGCACUUUACUAUACUAUAUAUCGCGCCUCUCAUUC----GCUUUGUUUGUUUUCUUUUUUCGCAACUAACUGCGAGAAAAUGAAAAUGAAUGCAACGCUCCAGCGAUUGCAGGGCA
.((((.......))))............((((..((.((----(((..(((..(((((((((((((((......)))))))))).)))))..)))((...))...))))).))..)))). ( -33.50)
>consensus
AAUAGCACUUUACUAUACUAUAUAUUGCGCCUCUCAUUC____GCUUUGUUUGUUUUCUUUUUUCGCAACUAACUGCGAGAAAAUGAAAAUGAAUGCAACGCUCCAGCGAUUGCAGGGCA
.((((.......))))............((((................((((((((((((((((((((......)))))))))).))))))))))(((((((....))).)))).)))). (-32.13 = -32.47 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:54 2006